250K Pots will make your pups sound warmer
500K Pots will make your pups sound brighter
When playing at full volume I notice a very discenable difference ... but that's just me.
You have to experiement with various combinations of wood, hollow vs. solid body, scale length, string gauge etc. to see which you like. You also have to factor in your amp and speakers. For instance, for a single coil guitar like a tele, there's a reason why most people use 250K pots, but if it's a semi-solid body you might want to try a 500K pot to get over the extra creaminess of the resonant body. Really is personal taste.
If your trying to decide what to use, I'd say start with whatever is traditional as your base, and work off of that.